Table 3.
Other replicated pQTMs.
| CpG | pQTM (this study) | PpQTM | BetapQTM | eQTM (BIOS) | PeQTM | BetaeQTM |
|---|---|---|---|---|---|---|
| cg10604476 (ICAM5) chr19:10,403,908 | ICAM5 (5124-69_3) chr19:10,400,657-10,407,454 | 6.09 × 10−25 | 0.356 | ENSG00000105376 ICAM5 | 2.22 × 10−9 | 0.186 |
| cg03650189 (ICAM5) chr19:10,405,083 | ICAM5 | 1.22 × 10−24 | 0.344 | ENSG00000105376 ICAM5 | 1.68 × 10−5 | 0.129 |
| cg22910295 (ICAM5) chr19:10,403,862 | ICAM5 | 3.72 × 10−24 | 0.339 | ENSG00000105376 ICAM5 | 2.37 × 10−6 | −0.134 |
| cg15011409 (ICAM5) chr19:10,405,226 | ICAM5 | 5.96 × 10−23 | 0.331 | ENSG00000105376 ICAM5 | 2.66 × 10−12 | 0.198 |
| cg21994045 (ICAM5) chr19:10,403,936 | ICAM5 | 4.18 × 10−17 | 0.291 | ENSG00000105376 ICAM5 | 1.21 × 10−5 | −0.148 |
| cg10773601 (CLEC11A) chr19:51,226,046 | CLEC11A (4500-50_2) chr19:51,226,586-51,228,974 | 8.06 × 10−27 | −0.341 | ENSG00000105472 CLEC11A | 1.06 × 10−71 | 0.424 |
| cg16651537 (CLEC11A) chr19:51,226,536 | CLEC11A | 1.67 × 10−24 | −0.326 | ENSG00000105472 CLEC11A | 3.54 × 10−63 | 0.434 |
| cg05575921 (AHRR) chr5:373,378 | PIGR (3216-2_2) chr1:207,101,863-207,119,811 | 8.08 × 10−16 | −0.264 | ENSG00000180104 EXOC3a | 1.19 × 10−6 | 0.063 |
| cg18419358 (n.a.) chr6:158,384,009 | GP1BA (4990-87_1) chr17:4,835,592-4,838,325 | 2.52 × 10−12 | 0.228 | n.a. | n.a. | n.a. |
| cg27535410 (PRTN3) chr19:846,354 | PRTN3 (3514-49_2) chr19:840,963-848,175 | 1.21 × 10−11 | −0.219 | n.a. | n.a. | n.a. |
| cg13028630 (C4B/C4A) chr6:31,964,754 | C4A/C4B (4481-34_2) chr6:31,937,353-32,079,643 | 1.38 × 10−11 | −0.246 | n.a. | n.a. | n.a. |
| cg09488502 (SIGLEC5) chr19:52,134,289 | SIGLEC14 (5125-6_3) chr19:52,145,806-52,150,054 | 4.89 × 10−11 | 0.220 | n.a. | n.a. | n.a. |
The p-value (PpQTM, linear regression) and regression coefficient (BetapQTM) from the discovery study are reported. The chromosomal position of the CpG sites and the related protein coding genes are given, together with the associated protein and SOMAmer identifiers (SeqId). The BIOS QTL server5 was used to identify overlapping CpG methylation to gene expression associations (eQTMs). The respective p-values (peQTM, linear regression) and regression coefficients (betaeQTM) of the association of the respective CpG and the transcript are reported. Some of the associations are located in cis, that is, the CpG and the blood circulating protein coding region were within 1 Mbp (e.g. CLEC11A and ICAM5), while others were located in trans (e.g. AHRR)
aThese genes belong to the same cytogenic band as those reported by Illumina as being regulated by the respective CpG sites and are within physical proximity (<21,000 and 5000 bp downstream, respectively)